Observations of Jupiter by Cassini/CIRS, acquired during the December 2000 flyby, provide the latitudinal distribution of HCN and CO ₂ in Jupiter's stratosphere with unprecedented spatial resolution and coverage. Following up on a preliminary study by Kunde et al. [Kunde, V.G., and 41 colleagues, 2004. Science 305, 1582-1587], the analysis of these observations leads to two unexpected results (i) the total HCN mass in Jupiter's stratosphere in 2000 was (6.0±1.5)×10 g, i.e., at least three times larger than measured immediately after the Shoemaker-Levy 9 (SL9) impacts in July 1994 and (ii) the latitudinal distributions of HCN and CO ₂ are strikingly different: while HCN exhibits a maximum at 45° S and a sharp decrease towards high Southern latitudes, the CO ₂ column densities peak over the South Pole. The total CO ₂ mass is (2.9±1.2)×10 g. A possible cause for the HCN mass increase is its production from the photolysis of NH ₃, although a problem remains because, while millimeter-wave observations clearly indicate that HCN is currently restricted to submillibar ( ˜0.3 mbar) levels, immediate post-impact infrared observations have suggested that most of the ammonia was present in the lower stratosphere near 20 mbar. HCN appears to be a good atmospheric tracer, with negligible chemical losses. Based on 1-dimensional (latitude) transport models, the HCN distribution is best interpreted as resulting from the combination of a sharp decrease (over an order of magnitude in K) of wave-induced eddy mixing poleward of 40° and an equatorward transport with ˜7 cms velocity. The CO ₂ distribution was investigated by coupling the transport model with an elementary chemical model, in which CO ₂ is produced from the conversion of water originating either from SL9 or from auroral input. The auroral source does not appear adequate to reproduce the CO ₂ peak over the South Pole, as required fluxes are unrealistically high and the shape of the CO ₂ bulge is not properly matched. In contrast, the CO ₂ distribution can be fit by invoking poleward transport with a ˜30 cms velocity and vigorous eddy mixing ( K=2×10 cms). While the vertical distribution of CO ₂ is not measured, the combined HCN and CO ₂ results imply that the two species reside at different stratospheric levels. Comparing with the circulation regimes predicted by earlier radiative-dynamical models of Jupiter's stratosphere, and with inferences from the ethane and acetylene stratospheric latitudinal distribution, we suggest that CO ₂ lies in the middle stratosphere near or below the 5-mbar level.